OEOverlay

class OEOverlay

Note

With the default settings, the OEOverlay optimizes both shape and color.

The OEOverlay defined an interface for overlap optimization between a reference object (a molecule, grid or a shape query) and a fit molecule conformers.

The OEOverlay class defines the following public methods:

BestOverlay
GetOverlayOptions
Overlay
SetupRef
SortedOverlay

Constructors

OEOverlay(opts: OEOverlayOptions = OEOverlayOptions()) -> OEOverlay
OEOverlay(arg2: OEOverlay) -> OEOverlay

Default and copy constructors.

Assignment operator.
BestOverlay
BestOverlay(score: OEBestOverlayScore, fitMol: OEMol,
            pred: OEBestOverlayScoreSorterPred = OEHighestTanimotoCombo()) -> bool
Method optimizes the overlay between the reference object and the fit molecule conformers, and returns the best result, sorted based on the binary predicate pred. The predicate has a default setting of OEHighestTanimotoCombo. The reference object must be set using the SetupRef method, prior to calling this method.

GetOverlayOptions
GetOverlayOptions() -> OEOverlayOptions
Returns a reference to the OEOverlayOptions instance as currently set. This defines options to calculate overlay.

Overlay
Overlay(fitMol: OEMol) -> Iterable[OEBestOverlayResults]
Method optimizes the overlay between the reference object and the fit molecule conformers. The reference object must be set using the SetupRef method, prior to calling this method.

See also

BestOverlay

SortedOverlay

SetupRef
SetupRef(argRefMol: Union[OEGraphMol,OEMol,OEQMol]) -> bool
SetupRef(argRefGrid: OEScalarGrid) -> bool
SetupRef(argQuery: OEShapeQuery) -> bool
These method defines the interface for setting up the reference system for the OEOverlay instance with a molecule, grid or a shape query.

SortedOverlay
SortedOverlay(fitmol: OEMol, maxHits: int,
              pred: OEBestOverlayScoreSorterPred = OEHighestTanimotoCombo()) -> Iterable[OEBestOverlayScore]
Method optimizes the overlay between the reference object and the fit molecule conformers, and returns the desired number of top hits defined by maxHits, sorted based on the binary predicate pred. The predicate has a default setting of OEHighestTanimotoCombo. The reference object must be set using the SetupRef method, prior to calling this method.

This method is specifically preferred over the Overlay method when working with molecules containing a large number of conformers, as the burden to store all the results associated with all the conformers can stress the memory limits of a machine.